Transcranial brain mapping techniques, such as functional near-infrared spectroscopy (fNIRS) and transcranial magnetic stimulation (TMS), have been playing an increasingly important role in studies of human brain functions. Given a brain function of interest, fNIRS probes and TMS coils should be properly placed on the scalp to ensure that the function is effectively measured or modulated. However, since brain activity is inside the skull and invisible to the researcher during placement, this blind targeting may cause the device to partially or completely miss the functional target, resulting in inconsistent experimental results and divergent clinical outcomes, especially when participants' structural MRI data are not available. To address this issue, we propose here a framework for targeting a designated function directly from the scalp. First, a functional brain atlas for the targeted brain function is constructed via a meta-analysis of large-scale functional magnetic resonance imaging datasets. Second, the functional brain atlas is presented on the scalp surface by using a transcranial mapping previously established from an structural MRI dataset (n ​= ​114), resulting in a novel functional transcranial brain atlas (fTBA). Finally, a low-cost, portable scalp-navigation system is used to localize the transcranial device on the individual's scalp with the guidance of the fTBA. To demonstrate the feasibility of the targeting framework, both fNIRS and TMS mapping experiments were conducted. The results show that fTBA-guided fNIRS positioning can detect functional activity with high sensitivity and specificity for working memory and motor systems; Moreover, compared with traditional TMS targeting approaches (e.g. the International 10-20 System and the conventional 5-cm rule), the fTBA suggested motor stimulation site is closesr to both the motor hotspot and the center of gravity of motor evoked potentials (MEP-COG). In summary, the proposed method unblinds the transcranial function targeting process using prior information, providing an effective and straightforward approach to transcranial brain mapping studies, especially those without participants' structural MRI data.